Christian Mertes
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/FRASER |
| Branch: RELEASE_3_11 |
| Last Commit: 0b8a9a0 |
| Last Changed Date: 2020-09-04 01:49:00 -0400 (Fri, 04 Sep 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:36 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE FRASER PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 638/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FRASER 1.0.2 Christian Mertes
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: FRASER |
| Version: 1.0.2 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FRASER.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings FRASER_1.0.2.tar.gz |
| StartedAt: 2020-10-17 04:11:11 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:27:37 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 985.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FRASER.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FRASER.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings FRASER_1.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/FRASER.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FRASER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FRASER' version '1.0.2'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'FRASER' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::selectSome'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateRangesWithTxDb: no visible binding for global variable
'uniqueID'
extractChromosomeLengths: no visible binding for global variable
'mapped'
extractChromosomes: no visible binding for global variable 'mapped'
getAnnotationFeature: no visible binding for global variable
'first_feature'
getAnnotationFeature: no visible binding for global variable
'other_features'
Undefined global functions or variables:
first_feature mapped other_features uniqueID
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/FRASER/libs/i386/FRASER.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/FRASER/libs/x64/FRASER.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
FRASER 34.55 1.94 38.06
counts 26.11 0.17 27.61
optimHyperParams 9.08 0.03 9.11
injectOutliers 8.03 0.00 8.04
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
FRASER 44.19 0.53 49.47
counts 27.33 0.32 29.19
optimHyperParams 9.86 0.05 9.91
injectOutliers 6.88 0.00 6.87
results 6.48 0.17 6.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/FRASER.Rcheck/00check.log'
for details.
FRASER.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/FRASER_1.0.2.tar.gz && rm -rf FRASER.buildbin-libdir && mkdir FRASER.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FRASER.buildbin-libdir FRASER_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL FRASER_1.0.2.zip && rm FRASER_1.0.2.tar.gz FRASER_1.0.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 945k 100 945k 0 0 12.4M 0 --:--:-- --:--:-- --:--:-- 13.5M
install for i386
* installing *source* package 'FRASER' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o FRASER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/FRASER.buildbin-libdir/00LOCK-FRASER/00new/FRASER/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'FRASER'
finding HTML links ... done
FRASER html
FraserDataSet-class html
FraserDataSet html
annotateRanges html
assayNames-FraserDataSet-method html
assays-FraserDataSet-method html
calculatePSIValues html
countRNA html
finding level-2 HTML links ... done
counts html
createTestFraserDataSet html
fds-methods html
filtering html
getter_setter_functions html
injectOutliers html
length-FraserDataSet-method html
loadFraserDataSet html
makeSimulatedFraserDataSet html
optimHyperParams html
plotFunctions html
psiTypes html
results html
subset html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'FRASER' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -DARMA_DONT_USE_OPENMP -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FRASER.dll tmp.def RcppExports.o loss_n_gradient_functions.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/FRASER.buildbin-libdir/FRASER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FRASER' as FRASER_1.0.2.zip
* DONE (FRASER)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'FRASER' successfully unpacked and MD5 sums checked
|
FRASER.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(FRASER)
Loading required package: BiocParallel
Loading required package: data.table
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:data.table':
first, second
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'FRASER'
The following object is masked from 'package:Biobase':
samples
The following object is masked from 'package:GenomeInfoDb':
mapSeqlevels
>
> # to speed up the testing on windows do it in serial mode
> if(.Platform$OS.type != "unix") {
+ register(SerialParam())
+ }
>
> test_check("FRASER")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o sample3.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4644 ... ||
|| Features : 87 ||
|| Meta-features : 87 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample3.bam... ||
|| Strand specific : stranded ||
|| Paired-end reads are included. ||
|| Total alignments : 1918 ||
|| Successfully assigned alignments : 241 (12.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o sample1.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4644 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample1.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 474 ||
|| Successfully assigned alignments : 145 (30.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o sample2.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4644 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample2.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 2455 ||
|| Successfully assigned alignments : 826 (33.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o sample3.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4644 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample3.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 1918 ||
|| Successfully assigned alignments : 703 (36.7%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
== testthat results ===========================================================
[ OK: 52 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 0 ]
>
> proc.time()
user system elapsed
96.50 3.35 107.59
|
FRASER.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(FRASER)
Loading required package: BiocParallel
Loading required package: data.table
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:data.table':
first, second
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'FRASER'
The following object is masked from 'package:Biobase':
samples
The following object is masked from 'package:GenomeInfoDb':
mapSeqlevels
>
> # to speed up the testing on windows do it in serial mode
> if(.Platform$OS.type != "unix") {
+ register(SerialParam())
+ }
>
> test_check("FRASER")
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o sample3.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4184 ... ||
|| Features : 87 ||
|| Meta-features : 87 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample3.bam... ||
|| Strand specific : stranded ||
|| Paired-end reads are included. ||
|| Total alignments : 1918 ||
|| Successfully assigned alignments : 241 (12.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o sample1.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4184 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample1.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 474 ||
|| Successfully assigned alignments : 145 (30.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o sample2.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4184 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample2.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 2455 ||
|| Successfully assigned alignments : 826 (33.6%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.2.6
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
|| o sample3.bam ||
|| ||
|| Annotation : R data.frame ||
|| Dir for temp files : C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmp ... ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Paired-end : yes ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 10 ||
|| ||
|| Chimeric reads : counted ||
|| Both ends mapped : not required ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file .Rsubread_UserProvidedAnnotation_pid4184 ... ||
|| Features : 77 ||
|| Meta-features : 77 ||
|| Chromosomes/contigs : 2 ||
|| ||
|| Process BAM file sample3.bam... ||
|| Paired-end reads are included. ||
|| Total alignments : 1918 ||
|| Successfully assigned alignments : 703 (36.7%) ||
|| Running time : 0.00 minutes ||
|| ||
|| Write the final count table. ||
|| Write the read assignment summary. ||
|| ||
\\============================================================================//
== testthat results ===========================================================
[ OK: 52 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
111.64 1.71 122.39
|
|
FRASER.Rcheck/examples_i386/FRASER-Ex.timings
|
FRASER.Rcheck/examples_x64/FRASER-Ex.timings
|